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teaching:2017summer:bioappgere

Practical Course: Bioinformatics Applications in Genome Research


392177 Dörr Summer semester 2017 Block 13.03.2017-24.03.2017 - 9:30-17:30 Uhr in V6-116 ekvv

Content

In this course, practical applications and issues in concrete problem statements and handling real data sets will be addressed. The following topics are intended: assembly, scaffolding, annotation, gene prediction, comparative analysis, etc.

Theoretical knowledge of the students shall be supplemented by practical aspects such as setting up and running existing tools, implementing small own tools, pre- and postprocessing, and critical interpretation of results. A continuously enriched visualization of the data and the obtained results will also guide through the course.

  • Requires participation in the lecture “Algorithms in Genome Research”.
  • Beside regular and active participation in the course, each student gives a short (15min) presentation and presents their results shall to other participants.

Overview

Date Topic Presentation Solution (for next day)
Mon, 13.3. Shell Dany: Introduction to Python Tilman
Tue, 14.3. Assembly Christian: Genome Assembly, de Brujin Graphs Christian
Wed, 15.3. Finishing Philipp: BWA Jens
Thu, 16.3. Genome rearrangements I Franzi: Rearrangement distances, Dany: Workflow management: snakemake Marcel
Fri, 17.3. Genome rearrangements II Tilman: Circos tutorial Philipp
Mon, 20.3. Gene Prediction Ago: Gene Prediction (software: Glimmer, Prodigal) Ago
Tue, 21.3. Hidden Markov Models (HMMs) Marcel: HMMs Franzi
Wed, 22.3. Position-Specific Scoring Matrices (PSSMs) Jens: PSSMs Tilman
Thu, 23.3. Metagenomics Philipp: Metagenomics
Fri, 24.3. Finishing the Circos plot

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teaching/2017summer/bioappgere.txt · Last modified: 2017/04/07 13:48 by Daniel Doerr